An ankle injury to Socceroos star Tim Cahill reduced Sydney FC's win over table-toppers Melbourne City to an afterthought.

Luke Wilkshire's first A-League goal gave the Sky Blues a 1-0 win on Friday night to put Graham Arnold's side on top of the competition for the first time this season.

The away fans celebrated the 60th-minute goal but, earlier at AAMI Park, the atmosphere was subdued.

An ankle knock to Cahill -- in his first club start of the season -- hushed the crowd, well aware this was his last match before heading to Honduras for do-or-die World Cup qualifiers.

The 37-year-old appeared to tweak his right ankle while hurdling Sydney FC defender Jordi Buijs during an innocuous challenge.

After playing on for several minutes, Cahill slumped to the ground and signalled for a substitution.

Scans will determine whether Cahill is able to represent his country in a week.

In any case, City felt his absence on Friday night against the A-League champions.

The Sky Blues looked a class above City, who had previously recorded four-straight wins for their best start to a campaign.

City gave up the lion's share of possession but both teams failed to score during a high-paced first half.

City talisman Nick Fitzgerald came closest, running through the midfield before receiving the ball back on the edge of the box and unleashing a shot that appeared destined for the corner of the net.

Ex-City goalkeeper Andrew Redmayne produced a world-class fingertip save in front of City's fans to preserve the deadlock.

Ross McCormack missed a tap-in from Fitzgerald's fine centre after halftime before Sydney FC made the breakthrough.

Michael Zullo, who left City last year, found Wilkshire at the back post with a deep cross, which the 36-year-old side footed off the pitch and past Eugene Galekovic.

Buijs made an added-time headed clearance to deny Iacopo La Rocca an equaliser, ensuring the Sky Blues overtook their title rivals at the top of table.

Arnold said his side was working at "45 percent" and would still get better.

"It was round five and we've got to go through the process for 27 rounds," he said.

"It's not an easy place to come. We were up against a team that had a lot of confidence [but] we had a strong belief and confidence."

Melbourne City coach Warren Joyce, who saw his side lose for the first time this season, said he was frustrated by a lack of concentration.

"I didn't see them causing a great deal of problems at all [in the first half]," he said. "Then we gave them too much room ... we gave them a goal with no one tracking runners. It's a poor goal to concede."